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<p>Base docs for the cudaaligner package (tbd)  
<a href="#details">More...</a></p>
<table class="memberdecls">
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Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">claragenomics::cudaaligner::Aligner</a></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html">claragenomics::cudaaligner::Alignment</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classclaragenomics_1_1cudaaligner_1_1Alignment.html" title="Alignment - Object encapsulating an alignment between 2 string.">Alignment</a> - Object encapsulating an alignment between 2 string.  <a href="classclaragenomics_1_1cudaaligner_1_1Alignment.html#details">More...</a><br /></td></tr>
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Typedefs</h2></td></tr>
<tr class="memitem:ga228dcdd4bf0cf40c64786cce6b045c40"><td class="memItemLeft" align="right" valign="top">typedef std::pair&lt; std::string, std::string &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">claragenomics::cudaaligner::FormattedAlignment</a></td></tr>
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<tr class="memitem:ga7d6424e11f69650b1d4eabef0cf4f602"><td class="memItemLeft" align="right" valign="top"><a id="ga7d6424e11f69650b1d4eabef0cf4f602"></a>enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">claragenomics::cudaaligner::StatusType</a> { <br />
&#160;&#160;<b>success</b> = 0, 
<b>uninitialized</b>, 
<b>exceeded_max_alignments</b>, 
<b>exceeded_max_length</b>, 
<br />
&#160;&#160;<b>exceeded_max_alignment_difference</b>, 
<b>generic_error</b>
<br />
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<tr class="memdesc:ga7d6424e11f69650b1d4eabef0cf4f602"><td class="mdescLeft">&#160;</td><td class="mdescRight">CUDA Aligner error type. <br /></td></tr>
<tr class="separator:ga7d6424e11f69650b1d4eabef0cf4f602"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gafcccbe51c86f9772ccf837fc433f518b"><td class="memItemLeft" align="right" valign="top"><a id="gafcccbe51c86f9772ccf837fc433f518b"></a>enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">claragenomics::cudaaligner::AlignmentType</a> { <b>global_alignment</b> = 0, 
<b>unset</b>
 }</td></tr>
<tr class="memdesc:gafcccbe51c86f9772ccf837fc433f518b"><td class="mdescLeft">&#160;</td><td class="mdescRight">AlignmentType - Enum for storing type of alignment. <br /></td></tr>
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<tr class="memitem:ga8ee40da066dcb49eb0516b6a763ec45d"><td class="memItemLeft" align="right" valign="top"><a id="ga8ee40da066dcb49eb0516b6a763ec45d"></a>enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudaaligner.html#ga8ee40da066dcb49eb0516b6a763ec45d">claragenomics::cudaaligner::AlignmentState</a> : int8_t { <b>match</b> = 0, 
<b>mismatch</b>, 
<b>insertion</b>, 
<b>deletion</b>
 }</td></tr>
<tr class="memdesc:ga8ee40da066dcb49eb0516b6a763ec45d"><td class="mdescLeft">&#160;</td><td class="mdescRight">AlignmentState - Enum for encoding each position in alignment. <br /></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:ga07b5416cfe8a05f326cb244f9d596449"><td class="memItemLeft" align="right" valign="top">std::unique_ptr&lt; <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudaaligner.html#ga07b5416cfe8a05f326cb244f9d596449">claragenomics::cudaaligner::create_aligner</a> (int32_t max_query_length, int32_t max_target_length, int32_t max_alignments, <a class="el" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a> type, cudaStream_t stream, int32_t device_id)</td></tr>
<tr class="memdesc:ga07b5416cfe8a05f326cb244f9d596449"><td class="mdescLeft">&#160;</td><td class="mdescRight">Created <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a> object.  <a href="group__cudaaligner.html#ga07b5416cfe8a05f326cb244f9d596449">More...</a><br /></td></tr>
<tr class="separator:ga07b5416cfe8a05f326cb244f9d596449"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga1d5dd3c4f48d7a735cbf6d7b5937d41a"><td class="memItemLeft" align="right" valign="top"><a id="ga1d5dd3c4f48d7a735cbf6d7b5937d41a"></a>
<a class="el" href="group__cudaaligner.html#ga7d6424e11f69650b1d4eabef0cf4f602">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudaaligner.html#ga1d5dd3c4f48d7a735cbf6d7b5937d41a">claragenomics::cudaaligner::Init</a> ()</td></tr>
<tr class="memdesc:ga1d5dd3c4f48d7a735cbf6d7b5937d41a"><td class="mdescLeft">&#160;</td><td class="mdescRight">Initialize CUDA <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a> context. <br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<p>Base docs for the cudaaligner package (tbd) </p>
<h2 class="groupheader">Typedef Documentation</h2>
<a id="ga228dcdd4bf0cf40c64786cce6b045c40"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ga228dcdd4bf0cf40c64786cce6b045c40">&#9670;&nbsp;</a></span>FormattedAlignment</h2>

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          <td class="memname"><a class="el" href="group__cudaaligner.html#ga228dcdd4bf0cf40c64786cce6b045c40">claragenomics::cudaaligner::FormattedAlignment</a></td>
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<p>Holds formatted strings representing an alignment. FormattedAlignment.first = formatted string for query FormattedAlignment.second = formatted string for target </p>

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<h2 class="groupheader">Function Documentation</h2>
<a id="ga07b5416cfe8a05f326cb244f9d596449"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ga07b5416cfe8a05f326cb244f9d596449">&#9670;&nbsp;</a></span>create_aligner()</h2>

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          <td class="memname">std::unique_ptr&lt;<a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a>&gt; claragenomics::cudaaligner::create_aligner </td>
          <td>(</td>
          <td class="paramtype">int32_t&#160;</td>
          <td class="paramname"><em>max_query_length</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int32_t&#160;</td>
          <td class="paramname"><em>max_target_length</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">int32_t&#160;</td>
          <td class="paramname"><em>max_alignments</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="group__cudaaligner.html#gafcccbe51c86f9772ccf837fc433f518b">AlignmentType</a>&#160;</td>
          <td class="paramname"><em>type</em>, </td>
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          <td class="paramkey"></td>
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          <td class="paramtype">cudaStream_t&#160;</td>
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          <td class="paramkey"></td>
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          <td class="paramtype">int32_t&#160;</td>
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          <td>)</td>
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<p>Created <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a> object. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">max_query_length</td><td>Maximum length of query string </td></tr>
    <tr><td class="paramname">max_target_length</td><td>Maximum length of target string </td></tr>
    <tr><td class="paramname">max_alignments</td><td>Maximum number of alignments to be performed </td></tr>
    <tr><td class="paramname">type</td><td>Type of aligner to construct </td></tr>
    <tr><td class="paramname">stream</td><td>CUDA Stream used for GPU interaction of the object </td></tr>
    <tr><td class="paramname">device_id</td><td>GPU device ID to run all CUDA operations on</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Unique pointer to <a class="el" href="classclaragenomics_1_1cudaaligner_1_1Aligner.html">Aligner</a> object </dd></dl>

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